1a.Objectives (from AD-416)
Objective 1: Identify a core set of molecular markers tailored for systematic characterization of the genetic diversity within and among Gossypium germplasm accessions that will be maintained under the sister project 6202-21000-032-00D.
Objective 2: Maintain and enhance CottonDB as a user-friendly tool for the cotton research community.
Sub-objective 2.A: Maintain and enhance CottonDB, including development of user friendly public interfaces.
Sub-objective 2.B: Develop bioinformatic software and tools to assist both users and curators of CottonDB.
Objective 3: Collaborate with other public sector researchers to construct and integrate physical and genetic maps of G. hirsutum.
Sub-objective 3.A: Develop cotton genetic maps that contain PCR-based DNA markers.
Sub-objective 3.B: Develop cotton physical maps that contain large-insert BAC clones.
Sub-objective 3.C: Integrate cotton genetic and physical maps with EST unigene information.
Objective 4: Identify key genes and genomic regions of cotton for use in developing cotton germplasm resources that exhibit desirable/improved agronomic and fiber traits.
Sub-objective 4.A: Apply genomic and bioinformatic tools to identify and characterize QTLs or alleles from cotton genetic resources, maintained under the sister project 6202-21000-032-00D, that govern key agronomic or fiber traits.
Sub-objective 4.B: Apply the preceding information to identify superior parents for developing breeding populations with novel sources of variability for traits of interest.
Sub-objective 4.C: Recombine and select the preceding breeding populations to accumulate desirable QTLs and alleles in enhanced cotton breeding lines.

1b.Approach (from AD-416)
To develop a portable core set of markers for cotton (Objective 1), new SSR and SNP markers will be developed from cotton BAC libraries and other genomic DNA templates. From the markers created, a core set of 208 markers will be carefully selected from the saturated genome map of tetraploid cotton (TM-1 x 3-79) with 8 markers from each of 26 chromosomes. Each of these core markers will have a high polymorphism information content (PIC) value to be determined on a standardized core germplasm panel consisting of 12 diverse Gossypium genotypes. These markers will be evenly distributed on the cotton genome, with every chromosome arm having 4 core markers at approximately 15-cM intervals. Data from marker development will be stored and made available in the CottonDB database. CottonDB, a tool for the research community, will be enhanced through continued migration of its information content to a relational structure, improved display pages, and direct record-to-record links between internet databases to integrate information into a larger virtual database (Objective 2). To enrich the delivered content and streamline users' searches for specific information, work will integrate related data from multiple databases. Solutions developed by other genome databases will be adapted and implemented to this project's databases where appropriate. To construct and integrate physical and genetic maps, genetic mapping of TM-1 BAC-derived and other markers will be conducted using the TM-1 x 3-79 RI population. Diagnostic DNA markers will be identified that are capable of detecting polymorphism in intraspecific populations, and these markers will be used to genotype the entire TM-1 x 3-79 RI mapping population. A score matrix will be generated from the genotyping experiments and merged with the existing mapping database to perform linkage analysis via MapMaker and/or JOINMAP software programs. Recombination frequencies will be converted into map distances (cM). Approximately 500 SSR and 500 SNP markers will be added to the existing genetic map that contains 1,200 SSR markers to obtain an average resolution of 1-2 cM per marker. Integration of cotton genetic and physical maps will be achieved by anchoring framework genetic markers to TM-1 BAC contigs, and locating BAC-derived markers to the TM-1 x 3-79 RI map (Objective 3). Comparisons of genetic and physical map tools (CMap and IntegratedMap) will allow for consolidation of all structural and physical genomic information. In order to utilize the growing numbers of QTLs reported in cotton, work will validate those QTL by aligning genomic locations and comparing genetic effects (Objective 4). Information for QTLs of interest will be related among comparable studies in cotton and will be obtained from a variety of sources, including published accounts and database records. Once specific chromosomal regions containing genes that make a significant contribution to the expression of a complex phenotype of interest are identified, fine-mapping of the most promising genomic regions will be used to identify polymorphisms in coding and/or regulatory regions.

3.Progress Report
Work under this project during FY 2009 progressed well in developing sophisticated molecular biology tools and techniques to better define the genetic diversity and its structure in cotton. The work developed additional tools known as DNA markers for use by project scientists and by others in identifying and locating genes in cotton that can be exploited to improve the crop. Significant progress was made in the development of genome maps for cotton, and in the identification of cotton genes that control fiber quality and other important traits affecting cotton growth and development. Project work revitalized the standardized cotton marker development (CMD) panel that is used by cotton researchers worldwide as a standard in their work. Project scientists and collaborators made significant progress in sequencing two cotton chromosomes. Project scientists also worked closely and productively with high-level Monsanto administrators and others in the cotton research community to release for public access important genetic markers (known as single sequence repeats or SSRs) that had been developed by Monsanto scientists. These markers will be of major value in facilitating the ongoing work of cotton researchers and breeders. All available information and data related to the Monsanto markers was uploaded into the Cotton DB database (maintained by the project) and to the major international database GenBank. Information in both of these databases is available to researchers worldwide, without restriction. Genetic tools for cotton, developed by the project, were shared with the broader cotton research community, often through CottonDB. The database CottonDB was improved in structure and content in FY 2009, with additional information on markers, genomic maps, and germplasm being added. This project continues as a world leader in developing new tools for cutting-edge cotton research that will help exploit the genetic makeup of the plant for development of better cotton varieties for use in all cotton-producing area of the world.

4.Accomplishments
1.
New Genetic Markers for Cotton: Molecular markers are sophisticated tools that can aid in locating and "marking" useful genes controlling important biological functions in living organisms. As applied to cotton research, certain types of molecular markers known as simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) can greatly improve the speed and efficiency of cotton improvement efforts by aiding in locating genes associated with traits such as fiber quality, yield, disease resistance, etc. In collaboration with industry and academic scientists, we have released for public use more than 3,000 SSR and SNP markers for cotton. The release of these markers will have significant impact on the cotton research and breeding communities in ongoing efforts focused on developing better varieties for cotton growers both in the U.S. and other countries.

2.
Sequencing the Upland Cotton Genome: The complete genetic information contained within each cell of a living organism is referred to as its genome. Using molecular biology tools to define the genome of important plant and animal species is critical in improving these species for the betterment of mankind. One means of "defining" a genome is to sequence its DNA. In collaboration with both U.S. and international scientists, we have developed and used appropriate genetic tools to sequence portions of two chromosomes of the cotton genome. This accomplishment has contributed very valuable information on the genetic makeup of cotton, and it provides foundational data and direction to ongoing efforts to sequence all the chromosomes of the cotton genome. Exploitation of the knowledge gained through detailed sequencing and definition of the cotton genome will greatly facilitate development of new, more productive, and more environmentally-adapted cotton varieties for use by U.S. cotton farmers.